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She's cooped up in her castle doing 'research' of some sort alongside Luna. There was this whole thing about "Not disturbing the princess's research" when they were trying to set the party up in the first place and is half of why Pinky is throwing the party where she is. (Lonely Hooves 1-42). She's trying to get the princesses to come outside and take a break.

The story has actually set itself up pretty well for either Luna and Twilight to show up and get their Royal Smite on as a 'the cavalry is here' moment....or is set up to keep Twilight out of the fight so the reaper wolf doesn't have to deal with an alicorn battlemage in order to do what he's trying to do.